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(-) Description

Title :  CRYSTAL STRUCTURE OF RITUXIMAB FAB IN COMPLEX WITH AN EPITOPE PEPTIDE
 
Authors :  J. Du, C. Zhong, J. Ding
Date :  06 Feb 07  (Deposition) - 10 Apr 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,H,L,P,Q
Biol. Unit 1:  H,L,P  (1x)
Biol. Unit 2:  A,B,Q  (1x)
Keywords :  Fab-Peptide Complex, Rituximab, Chimeric Antibody, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Du, H. Wang, C. Zhong, B. Peng, M. Zhang, B. Li, S. Huo, Y. Guo, J. Ding
Structural Basis For Recognition Of Cd20 By Therapeutic Antibody Rituximab
J. Biol. Chem. V. 282 15073 2007
PubMed-ID: 17395584  |  Reference-DOI: 10.1074/JBC.M701654200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LIGHT CHAIN OF THE RITUXIMAB FAB FRAGMENT
    ChainsL, B
    EngineeredYES
    Organism CommonHUMAN, HOUSE MOUSE
    Organism ScientificHOMO SAPIENS, MUS MUSCULUS
    Organism Taxid9606,10090
    Other DetailsTHE PROTEIN WAS PRODUCED AS A CHIMERIC FAB FRAGMENT. RESIDUES 1-106 IS FROM MURINE AND 107-213 IS FROM HUMAN.
    Other Details - SourceTHE ANTIBODY WAS PURCHASED FROM ROCHE.
    Strain,
 
Molecule 2 - HEAVY CHAIN OF THE RITUXIMAB FAB FRAGMENT
    ChainsH, A
    EngineeredYES
    Organism CommonHUMAN, HOUSE MOUSE
    Organism ScientificHOMO SAPIENS, MUS MUSCULUS
    Organism Taxid9606,10090
    Other DetailsTHE PROTEIN WAS PRODUCED AS A CHIMERIC FAB FRAGMENT. RESIDUES 1-121 IS FROM MURINE AND 122-224 IS FROM HUMAN.
    Other Details - SourceTHE ANTIBODY WAS PURCHASED FROM ROCHE.
    Strain,
 
Molecule 3 - B-LYMPHOCYTE ANTIGEN CD20
    ChainsP, Q
    EngineeredYES
    FragmentEPITOPE PEPTIDE
    Other DetailsTHE EPITOPE PEPTIDE WAS SYNTHESIZED AT SHANGHAI SCIENCE PEPTIDE BIOLOGICAL TECHNOLOGY
    SynonymMEMBRANE-SPANNING 4-DOMAINS SUBFAMILY A MEMBER 1, B-LYMPHOCYTE SURFACE ANTIGEN B1, LEU-16, BP35
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABHLPQ
Biological Unit 1 (1x)  HLP 
Biological Unit 2 (1x)AB   Q

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2OSL)

(-) Sites  (0, 0)

(no "Site" information available for 2OSL)

(-) SS Bonds  (11, 11)

Asymmetric Unit
No.Residues
1A:22 -A:96
2A:148 -A:204
3B:23 -B:87
4B:133 -B:193
5H:22 -H:96
6H:148 -H:204
7L:23 -L:87
8L:133 -L:193
9L:213 -H:224
10P:167 -P:183
11Q:167 -Q:183

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Ser L:7 -Pro L:8
2Asn L:93 -Pro L:94
3Tyr L:139 -Pro L:140
4Phe H:154 -Pro H:155
5Glu H:156 -Pro H:157
6Ser B:7 -Pro B:8
7Asn B:93 -Pro B:94
8Tyr B:139 -Pro B:140
9Phe A:154 -Pro A:155
10Glu A:156 -Pro A:157

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OSL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OSL)

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.4aENST000003899394aENSE00001507321chr11:60229654-60230006353CD20_HUMAN1-53530--
1.5ENST000003899395ENSE00001107914chr11:60230475-60230594120CD20_HUMAN54-93400--
1.6cENST000003899396cENSE00001507320chr11:60231761-6023181757CD20_HUMAN94-112190--
1.7cENST000003899397cENSE00001107910chr11:60233394-60233630237CD20_HUMAN113-191792P:167-186
Q:165-186
20
22
1.8bENST000003899398bENSE00001028073chr11:60234432-60234533102CD20_HUMAN192-225340--
1.9eENST000003899399eENSE00001107918chr11:60235723-602382252503CD20_HUMAN226-297720--

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2oslA01 A:1-121 Immunoglobulins                                                                                          2oslA02 A:122-221 Immunoglobulins                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee........eeee...eeeee........eeeee...........eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeee..........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2osl A   1 QVQLQQPGAELVKPGASVKMSCKASGYTFTSYNMHWVKQTPGRGLEWIGAIYPGNGDTSYNQKFKGKATLTADKSSSTAYMQLSSLTSEDSAVYYCARSTYYGGDWYFNVWGAGTTVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 

Chain B from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains -d2oslb1 B:2-106 Immunoglobulin light chain kappa variable domain, VL-kappa                               d2oslb2 B:107-213 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 2oslB01 B:1-107 Immunoglobulins                                                                            2oslB02 B:108-210 Immunoglobulins                                                                      --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh...eeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeee.hhhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2osl B   1 QIVLSQSPAILSASPGEKVTMTCRASSSVSYIHWFQQKPGSSPKPWIYATSNLASGVPVRFSGSGSGTSYSLTISRVEAEDAATYYCQQWTSNPPTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   

Chain H from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2oslH01 H:1-121 Immunoglobulins                                                                                          2oslH02 H:122-224 Immunoglobulins                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee......eeeee...eeeee........eeeee..........eeeeeeeeeee.....eeee........eee...ee.....eeeeeeeeee.hhhh....eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2osl H   1 QVQLQQPGAELVKPGASVKMSCKASGYTFTSYNMHWVKQTPGRGLEWIGAIYPGNGDTSYNQKFKGKATLTADKSSSTAYMQLSSLTSEDSAVYYCARSTYYGGDWYFNVWGAGTTVTVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC 224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    

Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains -d2osll1 L:2-106 Immunoglobulin light chain kappa variable domain, VL-kappa                               d2osll2 L:107-213 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 2oslL01 L:1-107 Immunoglobulins                                                                            2oslL02 L:108-210 Immunoglobulins                                                                      --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2osl L   1 QIVLSQSPAILSASPGEKVTMTCRASSSVSYIHWFQQKPGSSPKPWIYATSNLASGVPVRFSGSGSGTSYSLTISRVEAEDAATYYCQQWTSNPPTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   

Chain P from PDB  Type:PROTEIN  Length:20
 aligned with CD20_HUMAN | P11836 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:20
                                   176       186
           CD20_HUMAN   167 CEPANPSEKNSPSTQYCYSI 186
               SCOP domains -------------------- SCOP domains
               CATH domains -------------------- CATH domains
               Pfam domains -------------------- Pfam domains
         Sec.struct. author ....hhhhh.hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------- SAPs(SNPs)
                    PROSITE -------------------- PROSITE
               Transcript 1 Exon 1.7c            Transcript 1
                 2osl P 167 CEPANPSEKNSPSTQYCYSI 186
                                   176       186

Chain Q from PDB  Type:PROTEIN  Length:22
 aligned with CD20_HUMAN | P11836 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:22
                                   174       184  
           CD20_HUMAN   165 YNCEPANPSEKNSPSTQYCYSI 186
               SCOP domains ---------------------- SCOP domains
               CATH domains ---------------------- CATH domains
               Pfam domains ---------------------- Pfam domains
         Sec.struct. author ......hhhhh.hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------- SAPs(SNPs)
                    PROSITE ---------------------- PROSITE
               Transcript 1 Exon 1.7c [INCOMPLETE] Transcript 1
                 2osl Q 165 YNCEPANPSEKNSPSTQYCYSI 186
                                   174       184  

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric Unit

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2OSL)

(-) Gene Ontology  (29, 33)

Asymmetric Unit(hide GO term definitions)
Chain P,Q   (CD20_HUMAN | P11836)
molecular function
    GO:0023026    MHC class II protein complex binding    Interacting selectively and non-covalently with the class II major histocompatibility complex.
    GO:0005154    epidermal growth factor receptor binding    Interacting selectively and non-covalently with the epidermal growth factor receptor.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0042113    B cell activation    The change in morphology and behavior of a mature or immature B cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
    GO:0042100    B cell proliferation    The expansion of a B cell population by cell division. Follows B cell activation.
    GO:0006959    humoral immune response    An immune response mediated through a body fluid.
cellular component
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CD20_HUMAN | P118361s8b 3bky 3pp4
        IGHG1_HUMAN | P018571aj7 1aqk 1axs 1bey 1d5b 1d5i 1d6v 1dfb 1dn2 1e4k 1fc1 1fc2 1fcc 1gaf 1h3t 1h3u 1h3v 1h3w 1h3x 1h3y 1hkl 1hzh 1i7z 1l6x 1n7m 1op3 1oqo 1oqx 1pg7 1t83 1t89 1vge 2dts 2gj7 2i5y 2iwg 2j6e 2jb5 2jb6 2o5x 2o5y 2o5z 2qad 2ql1 2qqk 2qql 2qqn 2qr0 2r56 2rcj 2rcs 2vxq 2wah 3agv 3ave 3ay4 3b2u 3b2v 3bdy 3be1 3bky 3bn9 3bqu 3c08 3c09 3c2s 3cfj 3cfk 3csy 3d0l 3d0v 3d6g 3d85 3dj9 3dnk 3do3 3dro 3drq 3dvg 3dvn 3eyf 3eyo 3eyq 3fjt 3mcl 3o11 3ry6 3s7g 3sgj 3sgk 3tv3 3twc 3tyg 3u0w 3u7w 3u7y 3v7m 3v8c 3v95 3wjj 3wjl 3wkn 3wn5 4acp 4b7i 4bm7 4bsv 4bsw 4byh 4cdh 4d9q 4d9r 4dag 4dz8 4eow 4hix 4j12 4ku1 4lld 4llm 4llq 4n0u 4nqs 4nqt 4nqu 4nwt 4nwu 4o4y 4o51 4q6y 4q74 4q7d 4w4n 4w4o 4wi2 4wi3 4wi4 4wi5 4wi6 4wi7 4wi8 4wi9 4x4m 4x98 4x99 4xmp 4xny 4xnz 4xxd 4zne 5bw7 5c7k 5d4q 5d6d 5di8 5dj0 5dj2 5dj6 5dj8 5dja 5djc 5djd 5djx 5djy 5djz 5dk0 5dk2 5dvk 5dvl 5dvm 5dvn 5dvo 5gsq 5hsf 5hy9 5hye 5hyf 5hyi 5iq7 5iq9 5iw3 5iw6 5jih 5jii 5jik 5k33 5k8d 5kwg 5m3v 5v43 5v4e

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